| Variant ID: vg0317761629 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761629 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 80. )
AAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAACTGTTG[G/T]
AAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCATACTA
TAGTATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTT[C/A]
CAACAGTTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.90% | 2.20% | 4.15% | 59.80% | NA |
| All Indica | 2759 | 6.50% | 3.10% | 5.58% | 84.81% | NA |
| All Japonica | 1512 | 85.20% | 0.50% | 0.66% | 13.62% | NA |
| Aus | 269 | 3.30% | 1.90% | 8.92% | 85.87% | NA |
| Indica I | 595 | 5.40% | 0.50% | 4.54% | 89.58% | NA |
| Indica II | 465 | 7.70% | 3.70% | 3.23% | 85.38% | NA |
| Indica III | 913 | 5.80% | 4.40% | 8.43% | 81.38% | NA |
| Indica Intermediate | 786 | 7.40% | 3.30% | 4.45% | 84.86% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.70% | 0.80% | 1.79% | 33.73% | NA |
| Japonica Intermediate | 241 | 83.80% | 1.70% | 0.41% | 14.11% | NA |
| VI/Aromatic | 96 | 84.40% | 2.10% | 4.17% | 9.38% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 4.44% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761629 | G -> T | LOC_Os03g31190.1 | missense_variant ; p.Pro147Thr; MODERATE | nonsynonymous_codon ; P147T | Average:34.815; most accessible tissue: Minghui63 panicle, score: 59.629 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0317761629 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.815; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |